You're referring to the automatic colors the GBC and GBA applied to regular old GB games, right? Unfortunately, this is not possible. The coloring info for that is actually stored directly on the GBC BIOS itself, with each GB game having its own entry. The GBC BIOS has never been successfully dumped. Therefore, the only thing you can do is create your own palettes based off what they originally looked like.

If you go into the display options you'll find a few alternate color schemes you can use. Later versions of Goomba Color have support for the first few Super Gameboy palettes as well, which I usually find sufficient for most games.